Well, of course they were the same. The only thing that was different was the Light/Dark division. If you remove that, you have Skirmish again. And Skirmish always was the better option in order to get good gameplay, since you have truly random match ups.
As pointed out numerous times, Pantheon can get ridiculous due to a higher chance of doubles and triples on one team and "premades" can play together more easily in Pantheon.
Pantheon was always more popular though, but I don't really see why. Maybe it really is just because of its higher "prestige".